--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/inspect_eset.xml	Sun Sep 12 19:48:26 2021 +0000
@@ -0,0 +1,99 @@
+<tool id="music_inspect_eset" name="Inspect Expression Set Object" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
+      profile="20.05" license="GPL-3.0-or-later" >
+    <description>Inspect an ExpressionSet object by a variety of attributes</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+Rscript --vanilla '$__tool_directory__/scripts/inspect.R' '$conf'
+]]></command>
+    <configfiles>
+        <configfile name="conf" >
+
+null_str_vec = function(gstr){
+   tokens = unlist(as.vector(strsplit(gstr, split=",")))
+   if (length(tokens) == 0){
+      return(NULL)
+   }
+   if (length(tokens) == 1){
+      return(tokens[[1]])
+   }
+   return(tokens)
+}
+
+rds_eset = readRDS('$rds_eset')
+inspector = null_str_vec('$inspector')
+outfile_tab='$out_tab'
+
+        </configfile>
+    </configfiles>
+    <inputs>
+        <param name="rds_eset" label="ESet Dataset" type="data" format="rdata.eset" />
+        <param name="inspector" label="Inspect" type="select"
+               help="Inspect an aspect of the ESet dataset" >
+            <!-- See: https://www.rdocumentation.org/packages/Biobase/versions/2.32.0/topics/eSet -->
+            <option value="print" selected="true">General Information</option>
+            <option value="exprs" >Expression Data Table</option>
+            <option value="pData" >PhenoType Data Table</option>
+            <option value="fData" >Feature Data Table</option>
+            <option value="dims" >Dimension</option>
+            <option value="experimentData" />
+            <option value="signature" />
+            <option value="annotation" />
+            <option value="abstract" />
+        </param>
+    </inputs>
+    <outputs>
+        <data name="out_tab" format="tabular" label="${tool.name} on ${on_string}: Inspection Result" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1" >
+            <!-- Inspect 0 -->
+            <param name="rds_eset" value="EMTABesethealthy.subset.rds" />
+            <param name="inspector" value="print" />
+            <output name="out_tab" >
+                <assert_contents>
+                    <has_text text="sampleNames: AZ_A10 AZ_A11 ... HP1502401_K15 (250 total)" />
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1" >
+            <!-- Inspect 1 -->
+            <param name="rds_eset" value="EMTABesethealthy.subset.rds" />
+            <param name="inspector" value="pData" />
+            <output name="out_tab" >
+                <assert_contents>
+                    <has_n_columns n="5" />
+                    <has_text_matching expression="AZ_A10\s+1\s+Non T2D\s+1\s+5\s+delta" />
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1" >
+            <!-- Inspect 2 -->
+            <param name="rds_eset" value="EMTABesethealthy.subset.rds" />
+            <param name="inspector" value="dims" />
+            <output name="out_tab" >
+                <assert_contents>
+                    <has_n_columns n="1" />
+                    <has_text_matching expression="Samples\s+\d{1,4}"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+Inspect an ExpressionSet object by a variety of attributes, such as experimentData, phenotype data, and annotations.
+
+For more options and information, consult `the manual <http://www.bioconductor.org/packages/release/bioc/vignettes/Biobase/inst/doc/ExpressionSetIntroduction.pdf>`_ and the `rdocumentation <https://www.rdocumentation.org/packages/Biobase/versions/2.32.0/topics/ExpressionSet>`_
+.
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+            @misc{falcon2007introduction,
+            title={An introduction to bioconductor’s expressionset class},
+            author={Falcon, Seth and Morgan, Martin and Gentleman, Robert},
+            year={2007}
+            }
+        </citation>
+    </citations>
+</tool>
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